Tropical Cyclone Cempaka occurred on November 27, 2017 in the Indian Ocean, just south of Central Java. This incident induced high rainfall leading to flash floods in the southern part of Central Java, including Gunungsewu Karst Area. The highest rainfall recorded on November 28, 2017, in this area was 239 mm/day (Automatic Rainfall Recorder/ARR Station in Pindul Cave) and 341 mm/day (ARR Station in Tepus). The extreme rainfall also caused groundwater flood in Ngreneng Karst Window. This study aimed to analyze the mechanism of this flood. The results of the analysis showed that it was caused by water filling up the conduit passage in the entire Bribin-Baron underground river system. The flow of the conduit pushed the diffuse flow into the surface fast, and the water that came out of Ngreneng Karst Window was thereby clear. The inundation lasted for ten days and submerged up to 26.4 ha of the study area.